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Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. The dynamic impact of location and resection on the glioma CSF proteome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307463. [PMID: 38798641 PMCID: PMC11118641 DOI: 10.1101/2024.05.15.24307463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples, including anatomical location and post-surgical changes, remains unknown. To that end, pre- versus post-resection intracranial CSF samples were obtained at early (1-16 days; n=20) or delayed (86-153 days; n=11) timepoints for patients with glioma. Paired lumbar-versus-intracranial glioma CSF samples were also obtained (n=14). Using aptamer-based proteomics, we identify significant differences in the CSF proteome between lumbar, subarachnoid, and ventricular CSF. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome. Proteomic data are provided with individual clinical annotations as a resource for the field. One Sentence Summary Glioma cerebrospinal fluid (CSF) accessed intra-operatively and longitudinally via devices can reveal impacts of treatment and anatomical location.
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2
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Holmberg KO, Borgenvik A, Zhao M, Giraud G, Swartling FJ. Drivers Underlying Metastasis and Relapse in Medulloblastoma and Targeting Strategies. Cancers (Basel) 2024; 16:1752. [PMID: 38730706 PMCID: PMC11083189 DOI: 10.3390/cancers16091752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/12/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Medulloblastomas comprise a molecularly diverse set of malignant pediatric brain tumors in which patients are stratified according to different prognostic risk groups that span from very good to very poor. Metastasis at diagnosis is most often a marker of poor prognosis and the relapse incidence is higher in these children. Medulloblastoma relapse is almost always fatal and recurring cells have, apart from resistance to standard of care, acquired genetic and epigenetic changes that correlate with an increased dormancy state, cell state reprogramming and immune escape. Here, we review means to carefully study metastasis and relapse in preclinical models, in light of recently described molecular subgroups. We will exemplify how therapy resistance develops at the cellular level, in a specific niche or from therapy-induced secondary mutations. We further describe underlying molecular mechanisms on how tumors acquire the ability to promote leptomeningeal dissemination and discuss how they can establish therapy-resistant cell clones. Finally, we describe some of the ongoing clinical trials of high-risk medulloblastoma and suggest or discuss more individualized treatments that could be of benefit to specific subgroups.
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Affiliation(s)
- Karl O. Holmberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
| | - Anna Borgenvik
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA;
- Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
| | - Géraldine Giraud
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
- Department of Women and Child Health, Uppsala University, 75124 Uppsala, Sweden
- Department of Pediatric Hematology and Oncology, Uppsala University Children’s Hospital, 75185 Uppsala, Sweden
| | - Fredrik J. Swartling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden; (K.O.H.); (M.Z.); (G.G.)
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3
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Valerius AR, Webb MJ, Hammad N, Sener U, Malani R. Cerebrospinal Fluid Liquid Biopsies in the Evaluation of Adult Gliomas. Curr Oncol Rep 2024; 26:377-390. [PMID: 38488990 DOI: 10.1007/s11912-024-01517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
PURPOSE OF REVIEW This review aims to discuss recent research regarding the biomolecules explored in liquid biopsies and their potential clinical uses for adult-type diffuse gliomas. RECENT FINDINGS Evaluation of tumor biomolecules via cerebrospinal fluid (CSF) is an emerging technology in neuro-oncology. Studies to date have already identified various circulating tumor DNA, extracellular vesicle, micro-messenger RNA and protein biomarkers of interest. These biomarkers show potential to assist in multiple avenues of central nervous system (CNS) tumor evaluation, including tumor differentiation and diagnosis, treatment selection, response assessment, detection of tumor progression, and prognosis. In addition, CSF liquid biopsies have the potential to better characterize tumor heterogeneity compared to conventional tissue collection and CNS imaging. Current imaging modalities are not sufficient to establish a definitive glioma diagnosis and repeated tissue sampling via conventional biopsy is risky, therefore, there is a great need to improve non-invasive and minimally invasive sampling methods. CSF liquid biopsies represent a promising, minimally invasive adjunct to current approaches which can provide diagnostic and prognostic information as well as aid in response assessment.
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Affiliation(s)
| | - Mason J Webb
- Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Nouran Hammad
- Jordan University of Science and Technology School of Medicine, Irbid, Jordan
| | - Ugur Sener
- Department of Neurology, Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Rachna Malani
- University of UT - Huntsman Cancer Institute (Department of Neurosurgery), Salt Lake City, UT, USA
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4
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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5
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Qi D, Li J, Quarles CC, Fonkem E, Wu E. Assessment and prediction of glioblastoma therapy response: challenges and opportunities. Brain 2023; 146:1281-1298. [PMID: 36445396 PMCID: PMC10319779 DOI: 10.1093/brain/awac450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Jing Li
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Chad Quarles
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, College Station, TX 77843, USA
- Department of Oncology and LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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6
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Khristov V, Lin A, Freedman Z, Staub J, Shenoy G, Mrowczynski O, Rizk E, Zacharia B, Connor J. Tumor-Derived Biomarkers in Liquid Biopsy of Glioblastoma. World Neurosurg 2023; 170:182-194. [PMID: 36347463 DOI: 10.1016/j.wneu.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/07/2022]
Abstract
There is a pressing clinical need for minimally invasive liquid biopsies to supplement imaging in the treatment of glioblastoma. Diagnostic imaging is often difficult to interpret and the medical community is divided on distinguishing among complete response, partial response, stable disease, and progressive disease. A minimally invasive liquid biopsy would supplement imaging and clinical findings and has the capacity to be helpful in several ways: 1) diagnosis, 2) selection of patients for specific treatments, 3) tracking of treatment response, and 4) prognostic value. The liquid biome is the combination of biological fluids including blood, urine, and cerebrospinal fluid that contain small amounts of tumor cells, DNA/RNA coding material, peptides, and metabolites. Within the liquid biome, 2 broad categories of biomarkers can exist: tumor-derived, which can be directly traced to the tumor, and tumor-associated, which can be traced back to the response of the body to disease. Although tumor-associated biomarkers are promising liquid biopsy candidates, recent advances in biomarker enrichment and detection have allowed concentration on a new class of biomarker: tumor-derived biomarkers. This review focuses on making the distinction between the 2 biomarker categories and highlights promising new direction.
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Affiliation(s)
- Vladimir Khristov
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA.
| | - Andrea Lin
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Zachary Freedman
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Jacob Staub
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Ganesh Shenoy
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Oliver Mrowczynski
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Elias Rizk
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - Brad Zacharia
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
| | - James Connor
- Department of Neurosurgery, Penn State Hershey College of Medicne, Hershey, Pennsylvania, USA
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7
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Khristov V, Nesterova D, Trifoi M, Clegg T, Daya A, Barrett T, Tufano E, Shenoy G, Pandya B, Beselia G, Smith N, Mrowczynski O, Zacharia B, Waite K, Lathia J, Barnholtz-Sloan J, Connor J. Plasma IL13Rα2 as a novel liquid biopsy biomarker for glioblastoma. J Neurooncol 2022; 160:743-752. [DOI: 10.1007/s11060-022-04196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022]
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8
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Assessment of Serum Hypoxia Biomarkers Pre- and Post-radiotherapy in Patients with Brain Tumors. J Mol Neurosci 2022; 72:2303-2312. [PMID: 36121548 PMCID: PMC9726784 DOI: 10.1007/s12031-022-02065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/02/2022] [Indexed: 12/13/2022]
Abstract
Hypoxia is a prevalent hallmark of many malignant neoplasms. The aim was to assess the serum hypoxia biomarkers HIF-1α, VEGF, osteopontin, erythropoietin, caveolin-1, GLUT-1, and LDH pre- and post-radiotherapy in patients with brain tumors. The study was conducted on 120 subjects were divided into two groups: group I: 40 healthy volunteers as control group. Group II: 80 brain tumor patients were subdivided into glioblastoma subgroup: 40 glioblastoma patients, meningioma subgroup: 40 malignant meningioma patients. Two venous blood samples were collected from every patient prior to and following RT and one sample from controls. Biomarkers were assayed by ELISA. In glioblastoma subgroup, HIF-1α, VEGF, and LDH were significantly increased after RT. On the contrary, these biomarkers were significantly decreased after RT in malignant meningioma subgroup. Osteopontin was significantly increased after RT in both subgroups. Regarding erythropoietin, it was significantly decreased in both subgroups when compared to before RT. Caveolin-1 showed a significant increase in glioblastoma subgroup after RT comparing to before RT. GLUT-1 was significantly increased after RT in both subgroups comparing to before RT. Association of significant elevation of hypoxia biomarkers either pre- or post-RT with aggressive tumor such as glioblastoma indicates that, they are markers of malignancy and may have a role in tumor development and progression.
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9
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Bunda S, Zuccato JA, Voisin MR, Wang JZ, Nassiri F, Patil V, Mansouri S, Zadeh G. Liquid Biomarkers for Improved Diagnosis and Classification of CNS Tumors. Int J Mol Sci 2021; 22:4548. [PMID: 33925295 PMCID: PMC8123653 DOI: 10.3390/ijms22094548] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 12/22/2022] Open
Abstract
Liquid biopsy, as a non-invasive technique for cancer diagnosis, has emerged as a major step forward in conquering tumors. Current practice in diagnosis of central nervous system (CNS) tumors involves invasive acquisition of tumor biopsy upon detection of tumor on neuroimaging. Liquid biopsy enables non-invasive, rapid, precise and, in particular, real-time cancer detection, prognosis and treatment monitoring, especially for CNS tumors. This approach can also uncover the heterogeneity of these tumors and will likely replace tissue biopsy in the future. Key components of liquid biopsy mainly include circulating tumor cells (CTC), circulating tumor nucleic acids (ctDNA, miRNA) and exosomes and samples can be obtained from the cerebrospinal fluid, plasma and serum of patients with CNS malignancies. This review covers current progress in application of liquid biopsies for diagnosis and monitoring of CNS malignancies.
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Affiliation(s)
- Severa Bunda
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Jeffrey A. Zuccato
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Mathew R. Voisin
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Justin Z. Wang
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Farshad Nassiri
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Vikas Patil
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Sheila Mansouri
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
| | - Gelareh Zadeh
- MacFeeters-Hamilton Center for Neuro-Oncology Research, 4-305 Princess Margaret Cancer Research Tower, 101 College Street, Toronto, ON M5G 1L7, Canada; (S.B.); (J.A.Z.); (M.R.V.); (J.Z.W.); (F.N.); (V.P.); (S.M.)
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON M5T 2S8, Canada
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10
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Lara-Velazquez M, Zarco N, Carrano A, Phillipps J, Norton ES, Schiapparelli P, Al-kharboosh R, Rincon-Torroella J, Jeanneret S, Corona T, Segovia J, Jentoft ME, Chaichana KL, Asmann YW, Quiñones-Hinojosa A, Guerrero-Cazares H. Alpha 1-antichymotrypsin contributes to stem cell characteristics and enhances tumorigenicity of glioblastoma. Neuro Oncol 2021; 23:599-610. [PMID: 33249487 PMCID: PMC8041345 DOI: 10.1093/neuonc/noaa264] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Glioblastomas (GBMs) are the main primary brain tumors in adults with almost 100% recurrence rate. Patients with lateral ventricle proximal GBMs (LV-GBMs) exhibit worse survival compared to distal locations for unknown reasons. One hypothesis is the proximity of these tumors to the cerebrospinal fluid (CSF) and its chemical cues that can regulate cellular phenotype. We therefore investigated the role of CSF on GBM gene expression and the role of a CSF-induced gene, SERPINA3, in GBM malignancy in vitro and in vivo. METHODS We utilized human CSF and GBM brain tumor-initiating cells (BTICs). We determined the impact of SERPINA3 expression in glioma patients using The Cancer Genome Atlas (TCGA) database. SERPINA3 expression changes were evaluated at mRNA and protein levels. The effects of knockdown (KD) and overexpression (OE) of SERPINA3 on cell migration, viability and cell proliferation were evaluated. Stem cell characteristics on KD cells were evaluated by differentiation and colony formation experiments. Tumor growth was studied by intracranial and flank injections. RESULTS GBM-CSF increased BTIC migration accompanied by upregulation of the SERPINA3 gene. In patient samples and TCGA data, we observed SERPINA3 to correlate directly with brain tumor grade and indirectly with GBM patient survival. SERPINA3 KD induced a decrease in cell proliferation, migration, invasion, and stem cell characteristics, while SERPINA3 OE increased cell migration. In vivo, SERPINA3 KD BTICs showed increased survival in a murine model. CONCLUSIONS SERPINA3 plays a key role in GBM malignancy and its inhibition results in a better outcome using GBM preclinical models.
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Affiliation(s)
| | - Natanael Zarco
- Department of Neurosurgery, Mayo Clinic, Jacksonville, Florida, USA
| | | | | | - Emily S Norton
- PECEM, UNAM, Mexico City, Mexico
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Rawan Al-kharboosh
- PECEM, UNAM, Mexico City, Mexico
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Regenerative Sciences Training Program, Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Teresa Corona
- Clinical Laboratory of Neurodegenerative Diseases, National Institute of Neurology and Neurosurgery, Mexico City, Mexico
| | - Jose Segovia
- Department of Physiology, Biophysics and Neurosciences, Cinvestav-IPN, Mexico City, Mexico
| | - Mark E Jentoft
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida, USA
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11
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Schmid D, Warnken U, Latzer P, Hoffmann DC, Roth J, Kutschmann S, Jaschonek H, Rübmann P, Foltyn M, Vollmuth P, Winkler F, Seliger C, Felix M, Sahm F, Haas J, Reuss D, Bendszus M, Wildemann B, von Deimling A, Wick W, Kessler T. Diagnostic biomarkers from proteomic characterization of cerebrospinal fluid in patients with brain malignancies. J Neurochem 2021; 158:522-538. [PMID: 33735443 DOI: 10.1111/jnc.15350] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/23/2022]
Abstract
Recent technological advances in molecular diagnostics through liquid biopsies hold the promise to repetitively monitor tumor evolution and treatment response of brain malignancies without the need of invasive surgical tissue accrual. Here, we implemented a mass spectrometry-based protein analysis pipeline which identified hundreds of proteins in 251 cerebrospinal fluid (CSF) samples from patients with four types of brain malignancies (glioblastoma, lymphoma, brain metastasis, and leptomeningeal disease [LMD]) and from healthy individuals with a focus on glioblastoma in a retrospective and confirmatory prospective observational study. CSF proteome deregulation via disruption of the blood brain barrier appeared to be largely conserved across brain tumor entities. CSF analysis of glioblastoma patients identified two proteomic clusters that correlated with tumor size and patient survival. By integrating CSF data with proteomic analyses of matching glioblastoma tumor tissue and primary glioblastoma cells, we identified potential CSF biomarkers for glioblastoma, in particular chitinase-3-like protein 1 (CHI3L1) and glial fibrillary acidic protein (GFAP). Key findings were validated in a prospective cohort consisting of 35 glioma patients. Finally, in LMD patients who frequently undergo repeated CSF work-up, we explored our proteomic pipeline as a mean to profile consecutive CSF samples. Therefore, proteomic analysis of CSF in brain malignancies has the potential to reveal biomarkers for diagnosis and therapy monitoring.
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Affiliation(s)
- Dominic Schmid
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Medical Faculty, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Functional Proteome Analysis, DKFZ, Heidelberg, Germany
| | - Pauline Latzer
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Judith Roth
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kutschmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hannah Jaschonek
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Petra Rübmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martha Foltyn
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Vollmuth
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Winkler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Corinna Seliger
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Felix
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany
| | - Felix Sahm
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jürgen Haas
- Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Reuss
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Brigitte Wildemann
- Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Neuroimmunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, DKTK, DKFZ, Heidelberg, Germany.,Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Tobias Kessler
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology and Neurooncology Program at the National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
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12
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Desiderio C, Rossetti DV, Castagnola M, Massimi L, Tamburrini G. Adamantinomatous craniopharyngioma: advances in proteomic research. Childs Nerv Syst 2021; 37:789-797. [PMID: 32617710 DOI: 10.1007/s00381-020-04750-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/22/2023]
Abstract
BACKGROUND Many efforts have been performed in the last decade to accomplish the genomic and proteomic characterization of pediatric adamantinomatous craniopharyngioma with the purpose to elucidate the molecular mechanisms underlying the onset and development of this pediatric brain tumor, its high recurrence rate, and, although classified as a histologically benign neoplasm, its aggressive behavior. METHODS The focus of this review is to perform the new comparison of the proteomic profiles of the solid component and the intracystic fluid of adamantinomatous craniopharyngioma based on our previous results, obtained by both the top-down and the bottom-up proteomic approaches, to disclose differences and similarities, and to discuss the results in the context of the most recent literature. RESULTS AND CONCLUSIONS Proteins and peptides identified in the cyst fluid and in the solid component of adamantinomatous craniopharyngioma (AC) include beyond markers of inflammation (i.e., alpha-defensins), proteins involved in cell migration and protein degradation (i.e., beta-thymosin and ubiquitin peptides), whose main role might be in tumor growth and infiltration of the surrounding neural structures. These last appeared different in the solid components compared with the cyst fluid, missing their terminal part in the solid tissue, a feature generally associated to malignancies, which might represent a distinct molecular site for an aggressive behavior of AC.
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Affiliation(s)
- Claudia Desiderio
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", Consiglio Nazionale delle Ricerche, Largo F. Vito 1, 00168, Rome, Italy.
| | - Diana Valeria Rossetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Luca Massimi
- UOC Neurochirurgia Infantile, Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Università Cattolica del Sacro Cuore, Largo Gemelli 1, 00168, Rome, Italy
| | - Gianpiero Tamburrini
- UOC Neurochirurgia Infantile, Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Università Cattolica del Sacro Cuore, Largo Gemelli 1, 00168, Rome, Italy.
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13
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Chen L, Qin D, Guo X, Wang Q, Li J. Putting Proteomics Into Immunotherapy for Glioblastoma. Front Immunol 2021; 12:593255. [PMID: 33708196 PMCID: PMC7940695 DOI: 10.3389/fimmu.2021.593255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/25/2021] [Indexed: 12/11/2022] Open
Abstract
In glioblastoma, the most aggressive brain cancer, a complex microenvironment of heterogeneity and immunosuppression, are considerable hurdles to classify the subtypes and promote treatment progression. Treatments for glioblastoma are similar to standard therapies for many other cancers and do not effectively prolong the survival of patients, due to the unique location and heterogeneous characteristics of glioblastoma. Immunotherapy has shown a promising effect for many other tumors, but its application for glioma still has some challenges. The recent breakthrough of high-throughput liquid chromatography-mass spectrometry (LC-MS/MS) systems has allowed researchers to update their strategy for identifying and quantifying thousands of proteins in a much shorter time with lesser effort. The protein maps can contribute to generating a complete map of regulatory systems to elucidate tumor mechanisms. In particular, newly developed unicellular proteomics could be used to determine the microenvironment and heterogeneity. In addition, a large scale of differentiated proteins provides more ways to precisely classify tumor subtypes and construct a larger library for biomarkers and biotargets, especially for immunotherapy. A series of advanced proteomic studies have been devoted to the different aspects of immunotherapy for glioma, including monoclonal antibodies, oncolytic viruses, dendritic cell (DC) vaccines, and chimeric antigen receptor (CAR) T cells. Thus, the application of proteomics in immunotherapy may accelerate research on the treatment of glioblastoma. In this review, we evaluate the frontline applications of proteomics strategies for immunotherapy in glioblastoma research.
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Affiliation(s)
- Liangyu Chen
- Department of Proteomics, Tianjin Enterprise Key Laboratory of Clinical Multi-omics, Tianjin, China
| | - Di Qin
- Department of Proteomics, Tianjin Enterprise Key Laboratory of Clinical Multi-omics, Tianjin, China
| | - Xinyu Guo
- Department of Proteomics, Tianjin Enterprise Key Laboratory of Clinical Multi-omics, Tianjin, China
| | - Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, China
| | - Jie Li
- Department of Proteomics, Tianjin Enterprise Key Laboratory of Clinical Multi-omics, Tianjin, China
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14
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Mattox AK, Yan H, Bettegowda C. The potential of cerebrospinal fluid-based liquid biopsy approaches in CNS tumors. Neuro Oncol 2020; 21:1509-1518. [PMID: 31595305 PMCID: PMC6917400 DOI: 10.1093/neuonc/noz156] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cerebrospinal fluid (CSF) may be the best hope for minimally invasive diagnosis and treatment monitoring of central nervous system (CNS) malignancies. Discovery/validation of cell-free nucleic acid and protein biomarkers has the potential to revolutionize CNS cancer care, paving the way for presurgical evaluation, earlier detection of recurrence, and the selection of targeted therapies. While detection of mutations, changes in RNA and miRNA expression, epigenetic alterations, and elevations of protein levels have been detected in the CSF of patients with CNS tumors, most of these biomarkers remain unvalidated. In this review, we focus on the molecular changes that have been identified in a variety of CNS tumors and profile the approaches used to detect these alterations in clinical samples. We further emphasize the importance of systemic collection of CSF and the establishment of standardized collection protocols that will lead to better cross-study biomarker validation and hopefully FDA-approved clinical markers.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center, Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Radiation Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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15
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Wu J, Zhang J, Wei J, Zhao Y, Gao Y. Urinary biomarker discovery in gliomas using mass spectrometry-based clinical proteomics. Chin Neurosurg J 2020; 6:11. [PMID: 32922940 PMCID: PMC7398313 DOI: 10.1186/s41016-020-00190-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
Background Gliomas are the most common primary malignant brain tumors and have a poor prognosis. Early detection of gliomas is crucial to improve patient outcomes. Urine accumulates systematic body changes and thus serves as an excellent early biomarker source. Methods At the biomarker discovery phase, we performed a self-controlled proteomics analysis by comparing urine samples collected from five glioma patients at the time of tumor diagnosis and after surgical removal of the tumor. At the biomarker validation phase, we further validated some promising proteins using parallel reaction monitoring (PRM)-based targeted proteomics in another cohort, including glioma, meningioma, and moyamoya disease patients as well as healthy controls. Results Using label-free proteome quantitation (LFQ), we identified twenty-seven urinary proteins that were significantly changed after tumor resection, many of which have been previously associated with gliomas. The functions of these proteins were significantly enriched in the autophagy and angiogenesis, which are associated with glioma development. After targeted proteomics validation, we identified a biomarker panel (AACT, TSP4, MDHM, CALR, LEG1, and AHSG) with an area under the curve (AUC) value of 0.958 for the detection of gliomas. Interestingly, AACT, LEG1, and AHSG are also potential cerebrospinal fluid or blood biomarkers of gliomas. Conclusions Using LFQ and PRM proteome quantification, we identified candidate urinary protein biomarkers with the potential to detect gliomas. This study will also provide clues for future biomarker studies involving brain diseases.
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Affiliation(s)
- Jianqiang Wu
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730 China
| | - Jun Zhang
- Department of Neurosurgery, Peking University International Hospital, Peking University, Beijing, 102206 China
| | - Jing Wei
- Department of Biochemistry, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, School of Life Sciences, Beijing Normal University, No.19 Xinjiekouwai Street, Beijing, 100875 China
| | - Yuanli Zhao
- Department of Neurosurgery, Peking University International Hospital, Peking University, Beijing, 102206 China.,Department of Neurosurgery, Beijing Tian Tan Hospital, Capital Medical University; China National Clinical Research Center for Neurological Diseases, Beijing, 100050 China
| | - Youhe Gao
- Department of Biochemistry, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, School of Life Sciences, Beijing Normal University, No.19 Xinjiekouwai Street, Beijing, 100875 China
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16
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Current and Future Trends on Diagnosis and Prognosis of Glioblastoma: From Molecular Biology to Proteomics. Cells 2019; 8:cells8080863. [PMID: 31405017 PMCID: PMC6721640 DOI: 10.3390/cells8080863] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma multiforme is the most aggressive malignant tumor of the central nervous system. Due to the absence of effective pharmacological and surgical treatments, the identification of early diagnostic and prognostic biomarkers is of key importance to improve the survival rate of patients and to develop new personalized treatments. On these bases, the aim of this review article is to summarize the current knowledge regarding the application of molecular biology and proteomics techniques for the identification of novel biomarkers through the analysis of different biological samples obtained from glioblastoma patients, including DNA, microRNAs, proteins, small molecules, circulating tumor cells, extracellular vesicles, etc. Both benefits and pitfalls of molecular biology and proteomics analyses are discussed, including the different mass spectrometry-based analytical techniques, highlighting how these investigation strategies are powerful tools to study the biology of glioblastoma, as well as to develop advanced methods for the management of this pathology.
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17
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Liquid Biopsy in Glioblastoma: Opportunities, Applications and Challenges. Cancers (Basel) 2019; 11:cancers11070950. [PMID: 31284524 PMCID: PMC6679205 DOI: 10.3390/cancers11070950] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy represents a minimally invasive procedure that can provide similar information from body fluids to what is usually obtained from a tissue biopsy sample. Its implementation in the clinical setting might significantly renew the field of medical oncology, facilitating the introduction of the concepts of precision medicine and patient-tailored therapies. These advances may be useful in the diagnosis of brain tumors that currently require surgery for tissue collection, or to perform genetic tumor profiling for disease classification and guidance of therapy. In this review, we will summarize the most recent advances and putative applications of liquid biopsy in glioblastoma, the most common and malignant adult brain tumor. Moreover, we will discuss the remaining challenges and hurdles in terms of technology and biology for its clinical application.
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18
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Investigating the Protein Signature of Adamantinomatous Craniopharyngioma Pediatric Brain Tumor Tissue: Towards the Comprehension of Its Aggressive Behavior. DISEASE MARKERS 2019; 2019:3609789. [PMID: 31191748 PMCID: PMC6525946 DOI: 10.1155/2019/3609789] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 02/07/2023]
Abstract
Although histologically benign, adamantinomatous craniopharyngioma (AC) pediatric brain tumor is a locally aggressive disease that frequently determines symptoms and hormonal dysfunctions related to the mass effect on the surrounding structures. Another typical feature of this benign neoplasm is the presence of voluminous liquid cysts frequently associated with the solid component. Even if studies have been devoted to the proteomic characterization of the tumor intracystic fluid, poor explorations have been performed on its solid part, principally investigated by transcriptomics technologies. In the present study, seven specimens of AC whole tumor tissue have been analyzed by LC-MS for a preliminary assessment of the proteomic profile by a top-down/bottom-up integrated approach. Thymosin beta 4, ubiquitin, calmodulin, S100 proteins, prothymosin α isoform 2, alpha-defensins 1-4, and fragments largely belonging to vimentin, hemoglobin, and glial fibrillary acidic protein characterized the intact proteome. The identification of alpha-defensins, formerly characterized in AC intracystic fluid, reinforces the hypothesis of a role for inflammation in tumor pathogenesis. A total number of 1798 unique elements were identified by a bottom-up approach with a special focus on the 433 proteins commonly characterized in the 85.7% of the samples analyzed. Their gene ontology classification evidenced the involvement of the adherence system, intermediate filaments, and actin cytoskeleton in tumor pathogenesis and of elements part of the Wnt, FGF, and EGFR signaling pathways. In addition, proteins involved in calcium modulation, innate immunity, inflammation, CCKR and integrin signaling, and gonadotropin-releasing hormone receptor pathways were also outlined. Further than confirming proteomic data previously obtained on AC intracystic fluid, these results offer a preliminary overview of the AC whole tissue protein phenotype, adding new hints towards the comprehension of this still obscure pediatric brain tumor.
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19
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Wei J, Marisetty A, Schrand B, Gabrusiewicz K, Hashimoto Y, Ott M, Grami Z, Kong LY, Ling X, Caruso H, Zhou S, Wang YA, Fuller GN, Huse J, Gilboa E, Kang N, Huang X, Verhaak R, Li S, Heimberger AB. Osteopontin mediates glioblastoma-associated macrophage infiltration and is a potential therapeutic target. J Clin Invest 2018; 129:137-149. [PMID: 30307407 DOI: 10.1172/jci121266] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
Glioblastoma is highly enriched with macrophages, and osteopontin (OPN) expression levels correlate with glioma grade and the degree of macrophage infiltration; thus, we studied whether OPN plays a crucial role in immune modulation. Quantitative PCR, immunoblotting, and ELISA were used to determine OPN expression. Knockdown of OPN was achieved using complementary siRNA, shRNA, and CRISPR/Cas9 techniques, followed by a series of in vitro functional migration and immunological assays. OPN gene-deficient mice were used to examine the roles of non-tumor-derived OPN on survival of mice harboring intracranial gliomas. Patients with mesenchymal glioblastoma multiforme (GBM) show high OPN expression, a negative survival prognosticator. OPN is a potent chemokine for macrophages, and its blockade significantly impaired the ability of glioma cells to recruit macrophages. Integrin αvβ5 (ITGαvβ5) is highly expressed on glioblastoma-infiltrating macrophages and constitutes a major OPN receptor. OPN maintains the M2 macrophage gene signature and phenotype. Both tumor-derived and host-derived OPN were critical for glioma development. OPN deficiency in either innate immune or glioma cells resulted in a marked reduction in M2 macrophages and elevated T cell effector activity infiltrating the glioma. Furthermore, OPN deficiency in the glioma cells sensitized them to direct CD8+ T cell cytotoxicity. Systemic administration in mice of 4-1BB-OPN bispecific aptamers was efficacious, increasing median survival time by 68% (P < 0.05). OPN is thus an important chemokine for recruiting macrophages to glioblastoma, mediates crosstalk between tumor cells and the innate immune system, and has the potential to be exploited as a therapeutic target.
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Affiliation(s)
- Jun Wei
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anantha Marisetty
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brett Schrand
- Department of Microbiology & Immunology, Dodson Interdisciplinary Immunotherapy Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Konrad Gabrusiewicz
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuuri Hashimoto
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Martina Ott
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zacharia Grami
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ling-Yuan Kong
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaoyang Ling
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hillary Caruso
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Gregory N Fuller
- Neuropathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Huse
- Neuropathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eli Gilboa
- Department of Microbiology & Immunology, Dodson Interdisciplinary Immunotherapy Institute, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Nannan Kang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Roel Verhaak
- Jackson Laboratory of Genomic Medicine, Farmington, Connecticut, USA
| | - Shulin Li
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy B Heimberger
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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20
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Spreafico F, Bongarzone I, Pizzamiglio S, Magni R, Taverna E, De Bortoli M, Ciniselli CM, Barzanò E, Biassoni V, Luchini A, Liotta LA, Zhou W, Signore M, Verderio P, Massimino M. Proteomic analysis of cerebrospinal fluid from children with central nervous system tumors identifies candidate proteins relating to tumor metastatic spread. Oncotarget 2018; 8:46177-46190. [PMID: 28526811 PMCID: PMC5542258 DOI: 10.18632/oncotarget.17579] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS). Candidate proteins were identified with Fisher's exact test and/or a univariate logistic regression model. Reverse phase protein array (RPPA), Western blot (WB), and ELISA were used in the training set and in an independent set of CFS samples (60 cases, 14 controls) to validate our discovery findings. Among the 558 non-redundant proteins identified by LC-MS/MS, 147 were missing from the CSF database at http://www.biosino.org. Fourteen of the 26 final top-candidate proteins were chosen for validation with WB, RPPA and ELISA methods. Six proteins (type 1 collagen, insulin-like growth factor binding protein 4, procollagen C-endopeptidase enhancer 1, glial cell-line derived neurotrophic factor receptor α2, inter-alpha-trypsin inhibitor heavy chain 4, neural proliferation and differentiation control protein-1) revealed the ability to discriminate metastatic cases from controls. Combining a unique dataset of CSFs from pediatric CNS tumors with a novel enabling nanotechnology led us to identify CSF proteins potentially related to metastatic status.
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Affiliation(s)
- Filippo Spreafico
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Italia Bongarzone
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Ruben Magni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Elena Taverna
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maida De Bortoli
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara M Ciniselli
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Barzanò
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Veronica Biassoni
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Weidong Zhou
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Michele Signore
- Department of Hematology, Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maura Massimino
- Pediatric Oncology Unit, Department of Hematology and Pediatric Hematology-Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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21
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Verheul C, Kleijn A, Lamfers MLM. Cerebrospinal fluid biomarkers of malignancies located in the central nervous system. HANDBOOK OF CLINICAL NEUROLOGY 2018; 146:139-169. [PMID: 29110768 DOI: 10.1016/b978-0-12-804279-3.00010-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CNS malignancies include primary tumors that originate within the CNS as well as secondary tumors that develop as a result of metastatic cancer. The delicate nature of the nervous systems makes tumors located in the CNS notoriously difficult to reach, which poses several problems during diagnosis and treatment. CSF can be acquired relatively easy through lumbar puncture and offers an important compartment for analysis of cells and molecules that carry information about the malignant process. Such techniques have opened up a new field of research focused on the identification of specific biomarkers for several types of CNS malignancies, which may help in diagnosis and monitoring of tumor progression or treatment response. Biomarkers are sought in DNA, (micro)RNA, proteins, exosomes and circulating tumor cells in the CSF. Techniques are rapidly progressing to assess these markers with increasing sensitivity and specificity, and correlations with clinical parameters are being investigated. It is expected that these efforts will, in the near future, yield clinically relevant markers that aid in diagnosis, monitoring and (tailored) treatment of patients bearing CNS tumors. This chapter provides a summary of the current state of affairs of the field of biomarkers of different types of CNS tumors.
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Affiliation(s)
- Cassandra Verheul
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anne Kleijn
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Martine L M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Rotterdam, the Netherlands.
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22
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Gahoi N, Malhotra D, Moiyadi A, Varma SG, Gandhi MN, Srivastava S. Multi-pronged proteomic analysis to study the glioma pathobiology using cerebrospinal fluid samples. Proteomics Clin Appl 2017; 12:e1700056. [PMID: 28679024 DOI: 10.1002/prca.201700056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/14/2017] [Accepted: 06/30/2017] [Indexed: 11/10/2022]
Abstract
PURPOSE Gliomas are one of the most aggressive and lethal brain tumors arising from neoplastic transformation of astrocytes and oligodendrocytes. A comprehensive quantitative analysis of proteome level differences in cerebrospinal fluid (CSF) across different grades of gliomas for a better understanding of glioma pathobiology is carried out. EXPERIMENTAL DESIGN Glioma patients are diagnosed by radiology and histochemistry-based analyses. Differential proteomic analysis of high (n = 12) and low (n = 5) grade gliomas, and control (n = 3) samples is performed by using two complementary quantitative proteomic approaches; 2D-DIGE and iTRAQ. Further, comparative analysis of three IDH wild-type and five IDH mutants is performed to identify the proteome level differences between these two sub-classes. RESULTS Level of several proteins including haptoglobin, transthyretin, osteopontin, vitronectin, complement factor H and different classes of immunoglobulins are found to be considerably increased in CSF of higher grades of gliomas. Subsequent bioinformatics analysis indicated that many of the dysregulated CSF proteins are associated with metabolism of lipids and lipoproteins, complement and coagulation cascades and extracellular matrix remodeling in gliomas. Intriguingly, CSF of glioma patients with IDH mutations exhibite increased levels of multiple proteins involved in response to oxidative stress. CONCLUSION AND CLINICAL RELEVANCE To the best of our knowledge, this is the foremost proteome level investigation describing comprehensive proteome profiles of different grades of gliomas using proximal fluid (CSF); and thereby providing insights into disease pathobiology, which aided in identification of grade and sub-type specific alterations. Moreover, if validated in larger clinical cohorts, a panel of differentially abundant CSF proteins may serve as potential disease monitoring and prognostic markers for gliomas.
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Affiliation(s)
- Nikita Gahoi
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.,Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Darpan Malhotra
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.,Department of Biochemistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, Alberta, Canada
| | | | - Santosh G Varma
- Dept. of Biochemistry, Grant Govt. Medical College and Sir JJ Group of Hospitals, Byculla, Mumbai, India.,BJ Medical College & Sassoon Hospital, Jai Prakash Narayan Road, Near Pune Railway Station, Pune, Maharashtra, India
| | - Mayuri N Gandhi
- Centre for Research in Nanotechnology and Sciences, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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23
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Lewandowska AE, Macur K, Czaplewska P, Liss J, Łukaszuk K, Ołdziej S. Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC-MS and SWATH Methodology. J Proteome Res 2017; 16:3053-3067. [PMID: 28658951 DOI: 10.1021/acs.jproteome.7b00366] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small-scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient-specific. Ultrafiltration was used to fractionate hFF to high-molecular-weight (HMW) proteome (>10 kDa) and low-molecular-weight (LMW) peptidome (<10 kDa) fractions. HMW and LMW compositions were analyzed using LC-MS in SWATH data acquisition and processing methodology. In total we were able to identify 158 proteins, from which 59 were never reported before as hFF components. 55 (45 not reported before) proteins were found by analyzing LMW fraction, 67 (14 not reported before) were found by analyzing HMW fraction, and 36 were identified in both fractions of hFF. We were able to perform quantitative analysis for 72 proteins from HMW fraction of hFF. We found that concentrations of 11 proteins varied substantially among hFF samples from single donors, and those proteins are promising targets to identify biomarkers useful in oocyte quality assessment.
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Affiliation(s)
- Aleksandra E Lewandowska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Katarzyna Macur
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
| | - Joanna Liss
- INVICTA Fertility and Reproductive Center , Trzy Lipy 3, 80-172 Gdańsk, Gdańsk, Poland
| | - Krzysztof Łukaszuk
- INVICTA Fertility and Reproductive Center , Trzy Lipy 3, 80-172 Gdańsk, Gdańsk, Poland.,Department of Obstetrics and Gynecological Nursing, Faculty of Health Sciences, Medical University of Gdańsk , Dębinki 7, 80-211 Gdańsk, Gdańsk, Poland
| | - Stanisław Ołdziej
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk , Abrahama 58, 80-307 Gdańsk, Gdańsk, Poland
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24
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Bastos P, Ferreira R, Manadas B, Moreira PI, Vitorino R. Insights into the human brain proteome: Disclosing the biological meaning of protein networks in cerebrospinal fluid. Crit Rev Clin Lab Sci 2017; 54:185-204. [PMID: 28393582 DOI: 10.1080/10408363.2017.1299682] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers. Bioinformatics analysis of data retrieved from 99 mass spectrometry (MS)-based studies on CSF profiling highlighted 1985 differentially expressed proteins across 49 diseases. A large percentage of the modulated proteins originate from exosome vesicles, and the majority are involved in either neuronal cell growth, development, maturation, migration, or neurotransmitter-mediated cellular communication. Nevertheless, some diseases present a unique CSF proteome profile, which were critically analyzed in the present study. For instance, 48 proteins were found exclusively upregulated in the CSF of patients with Alzheimer's disease and are mainly involved in steroid esterification and protein activation cascade processes. A higher number of exclusively upregulated proteins were found in the CSF of patients with multiple sclerosis (76 proteins) and with bacterial meningitis (70 proteins). Whereas in multiple sclerosis, these proteins are mostly involved in the regulation of RNA metabolism and apoptosis, in bacterial meningitis the exclusively upregulated proteins participate in inflammation and antibacterial humoral response, reflecting disease pathogenesis. The exploration of the contribution of exclusively upregulated proteins to disease pathogenesis will certainly help to envision potential biomarkers in the CSF for the clinical management of nervous system diseases.
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Affiliation(s)
- Paulo Bastos
- a Department of Chemistry , University of Aveiro , Aveiro , Portugal.,b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal
| | - Rita Ferreira
- c QOPNA, Department of Chemistry , University of Aveiro , Aveiro , Portugal
| | - Bruno Manadas
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal
| | - Paula I Moreira
- d CNC, Center for Neuroscience and Cell Biology, University of Coimbra , Coimbra , Portugal.,e Laboratory of Physiology, Faculty of Medicine , University of Coimbra , Coimbra , Portugal
| | - Rui Vitorino
- b Department of Medical Sciences , Institute for Biomedicine - iBiMED, University of Aveiro , Aveiro , Portugal.,f Departmento de Cirurgia e Fisiologia, Faculdade de Medicina , Unidade de Investigação Cardiovascular, Universidade do Porto , Porto , Portugal
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25
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Galicia N, Dégano R, Díez P, González-González M, Góngora R, Ibarrola N, Fuentes M. CSF analysis for protein biomarker identification in patients with leptomeningeal metastases from CNS lymphoma. Expert Rev Proteomics 2017; 14:363-372. [DOI: 10.1080/14789450.2017.1307106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- N. Galicia
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Dégano
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - P. Díez
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. González-González
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Góngora
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - N. Ibarrola
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. Fuentes
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
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26
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Proteomic Biomarker Identification in Cerebrospinal Fluid for Leptomeningeal Metastases with Neurological Complications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 974:85-96. [PMID: 28353226 DOI: 10.1007/978-3-319-52479-5_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Leptomeningeal metastases (LM) from solid tumours, lymphoma and leukaemia are characterized by multifocal neurological deficits with a high mortality rate. Early diagnosis and initiation of treatment are essential to kerb neurological deterioration. However, this is not always possible as 25% of cerebrospinal fluid samples produce false-negative results at first cytological examination. The identification of biomarkers that allow stratification of individuals according to risk for developing LM would be a major benefit. Proteomic-based approaches are now in increasing use for this purpose, and these are reviewed in this chapter with a focus on cerebrospinal fluid (CSF) analyses. The construction of a CSF proteome disease database would also facilitate analysis of other neurological disorders.
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27
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Touat M, Duran-Peña A, Alentorn A, Lacroix L, Massard C, Idbaih A. Emerging circulating biomarkers in glioblastoma: promises and challenges. Expert Rev Mol Diagn 2016; 15:1311-23. [PMID: 26394701 DOI: 10.1586/14737159.2015.1087315] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Glioblastoma (GBM) is the most common and devastating primary malignant brain tumor in adults. The past few years have seen major progress in our understanding of the molecular basis of GBM. These advances, which have contributed to the development of novel targeted therapies, will change the paradigms in GBM therapy from disease-based to individually tailored molecular target-based treatment. No validated circulating biomarkers have yet been integrated into clinical practice for GBM. There is thus a critical need to implement minimally invasive clinical tests enabling molecular stratification and prognosis assessment, as well as the prediction and monitoring of treatment response. After examination of data from recent studies exploring several categories of tumor-associated biomarkers (circulating tumor cells, extracellular vesicles, nucleic acids and oncometabolites) identified in the blood, cerebrospinal fluid and urine, this article discusses the challenges and prospects for the development of circulating biomarkers in GBM.
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Affiliation(s)
- Mehdi Touat
- a 1 Inserm U981, Université Paris Sud, Gustave Roussy, F-94805 Villejuif, France.,b 2 Département d'innovations thérapeutiques précoces, Gustave Roussy, F-94805 Villejuif, France
| | - Alberto Duran-Peña
- c 3 AP-HP, Hôpital Universitaire la Pitié Salpêtrière, Service de Neurologie 2-Mazarin, F-75013, Paris, France
| | - Agusti Alentorn
- c 3 AP-HP, Hôpital Universitaire la Pitié Salpêtrière, Service de Neurologie 2-Mazarin, F-75013, Paris, France.,d 4 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
| | - Ludovic Lacroix
- a 1 Inserm U981, Université Paris Sud, Gustave Roussy, F-94805 Villejuif, France.,e 5 Département de biologie médicale et de pathologie, Gustave Roussy, F-94805 Villejuif, France.,f 6 Laboratoire de recherche translationnelle et centre de ressources biologiques, Gustave Roussy, F-94805 Villejuif, France
| | - Christophe Massard
- a 1 Inserm U981, Université Paris Sud, Gustave Roussy, F-94805 Villejuif, France.,b 2 Département d'innovations thérapeutiques précoces, Gustave Roussy, F-94805 Villejuif, France
| | - Ahmed Idbaih
- c 3 AP-HP, Hôpital Universitaire la Pitié Salpêtrière, Service de Neurologie 2-Mazarin, F-75013, Paris, France.,d 4 Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
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28
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Ellis HP, Greenslade M, Powell B, Spiteri I, Sottoriva A, Kurian KM. Current Challenges in Glioblastoma: Intratumour Heterogeneity, Residual Disease, and Models to Predict Disease Recurrence. Front Oncol 2015; 5:251. [PMID: 26636033 PMCID: PMC4644939 DOI: 10.3389/fonc.2015.00251] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/29/2015] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma (GB) is the most common primary malignant brain tumor, and despite the availability of chemotherapy and radiotherapy to combat the disease, overall survival remains low with a high incidence of tumor recurrence. Technological advances are continually improving our understanding of the disease, and in particular, our knowledge of clonal evolution, intratumor heterogeneity, and possible reservoirs of residual disease. These may inform how we approach clinical treatment and recurrence in GB. Mathematical modeling (including neural networks) and strategies such as multiple sampling during tumor resection and genetic analysis of circulating cancer cells, may be of great future benefit to help predict the nature of residual disease and resistance to standard and molecular therapies in GB.
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Affiliation(s)
- Hayley P Ellis
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol , Bristol , UK
| | - Mark Greenslade
- Bristol Genetics Laboratory, North Bristol NHS Trust , Bristol , UK
| | - Ben Powell
- School of Mathematics, University of Bristol , Bristol , UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research , London , UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research , London , UK
| | - Kathreena M Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol , Bristol , UK
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29
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Adamczyk LA, Williams H, Frankow A, Ellis HP, Haynes HR, Perks C, Holly JMP, Kurian KM. Current Understanding of Circulating Tumor Cells - Potential Value in Malignancies of the Central Nervous System. Front Neurol 2015; 6:174. [PMID: 26322014 PMCID: PMC4530310 DOI: 10.3389/fneur.2015.00174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/24/2015] [Indexed: 12/23/2022] Open
Abstract
Detection of circulating tumor cells (CTCs) in the blood via so-called "liquid biopsies" carries enormous clinical potential in malignancies of the central nervous system (CNS) because of the potential to follow disease evolution with a blood test, without the need for repeat neurosurgical procedures with their inherent risk of patient morbidity. To date, studies in non-CNS malignancies, particularly in breast cancer, show increasing reproducibility of detection methods for these rare tumor cells in the circulation. However, no method has yet received full recommendation to use in clinical practice, in part because of lack of a sufficient evidence base regarding clinical utility. In CNS malignancies, one of the main challenges is finding a suitable biomarker for identification of these cells, because automated systems, such as the widely used Cell Search system, are reliant on markers, such as the epithelial cell adhesion molecule, which are not present in CNS tumors. This review examines methods for CTC enrichment and detection, and reviews the progress in non-CNS tumors and the potential for using this technique in human brain tumors.
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Affiliation(s)
- Lukasz A Adamczyk
- Department of Cellular Pathology, North Bristol NHS Trust , Bristol , UK
| | - Hannah Williams
- Brain Tumor Research Group, Institute of Clinical Neuroscience, North Bristol NHS Trust , Bristol , UK
| | - Aleksandra Frankow
- IGF and Metabolic Endocrinology Group, School of Clinical Sciences, North Bristol NHS Trust, University of Bristol , Bristol , UK
| | - Hayley Patricia Ellis
- Brain Tumor Research Group, Institute of Clinical Neuroscience, North Bristol NHS Trust , Bristol , UK
| | - Harry R Haynes
- Brain Tumor Research Group, Institute of Clinical Neuroscience, North Bristol NHS Trust , Bristol , UK
| | - Claire Perks
- IGF and Metabolic Endocrinology Group, School of Clinical Sciences, North Bristol NHS Trust, University of Bristol , Bristol , UK
| | - Jeff M P Holly
- IGF and Metabolic Endocrinology Group, School of Clinical Sciences, North Bristol NHS Trust, University of Bristol , Bristol , UK
| | - Kathreena M Kurian
- Brain Tumor Research Group, Institute of Clinical Neuroscience, North Bristol NHS Trust , Bristol , UK
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30
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Carlsson SK, Brothers SP, Wahlestedt C. Emerging treatment strategies for glioblastoma multiforme. EMBO Mol Med 2015; 6:1359-70. [PMID: 25312641 PMCID: PMC4237465 DOI: 10.15252/emmm.201302627] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Glioblastoma multiforme (GBM) is the deadliest form of brain tumor with a more than 90% 5-year mortality. GBM has a paltry median survival of 12.6 months attributed to the unique treatment limitations such as the high average age of onset, tumor location, and poor current understandings of the tumor pathophysiology. The resection techniques, chemotherapic strategies, and radiation therapy currently used to treat GBM have slowly evolved, but the improvements have not translated to marked increases in patient survival. Here, we will discuss the recent progress in our understanding of GBM pathophysiology, and the diagnostic techniques and treatment options. The discussion will include biomarkers, tumor imaging, novel therapies such as monoclonal antibodies and small-molecule inhibitors, and the heterogeneity resulting from the GBM cancer stem cell population.
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Affiliation(s)
- Steven K Carlsson
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shaun P Brothers
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation University of Miami Miller School of Medicine, Miami, FL, USA
| | - Claes Wahlestedt
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation University of Miami Miller School of Medicine, Miami, FL, USA
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31
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Liquid biopsies in patients with diffuse glioma. Acta Neuropathol 2015; 129:849-65. [PMID: 25720744 PMCID: PMC4436687 DOI: 10.1007/s00401-015-1399-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 12/18/2022]
Abstract
Diffuse gliomas are the most common malignant primary tumors of the central nervous system. Like other neoplasms, these gliomas release molecular information into the circulation. Tumor-derived biomarkers include proteins, nucleic acids, and tumor-derived extracellular vesicles that accumulate in plasma, serum, blood platelets, urine and/or cerebrospinal fluid. Recently, also circulating tumor cells have been identified in the blood of glioma patients. Circulating molecules, vesicles, platelets, and cells may be useful as easily accessible diagnostic, prognostic and/or predictive biomarkers to guide patient management. Thereby, this approach may help to circumvent problems related to tumor heterogeneity and sampling error at the time of diagnosis. Also, liquid biopsies may allow for serial monitoring of treatment responses and of changes in the molecular characteristics of gliomas over time. In this review, we summarize the literature on blood-based biomarkers and their potential value for improving the management of patients with a diffuse glioma. Incorporation of the study of circulating molecular biomarkers in clinical trials is essential for further assessment of the potential of liquid biopsies in this context.
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32
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Kros JM, Mustafa DM, Dekker LJM, Sillevis Smitt PAE, Luider TM, Zheng PP. Circulating glioma biomarkers. Neuro Oncol 2014; 17:343-60. [PMID: 25253418 DOI: 10.1093/neuonc/nou207] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 07/13/2014] [Indexed: 02/06/2023] Open
Abstract
Validated biomarkers for patients suffering from gliomas are urgently needed for standardizing measurements of the effects of treatment in daily clinical practice and trials. Circulating body fluids offer easily accessible sources for such markers. This review highlights various categories of tumor-associated circulating biomarkers identified in blood and cerebrospinal fluid of glioma patients, including circulating tumor cells, exosomes, nucleic acids, proteins, and oncometabolites. The validation and potential clinical utility of these biomarkers is briefly discussed. Although many candidate circulating protein biomarkers were reported, none of these have reached the required validation to be introduced for clinical practice. Recent developments in tracing circulating tumor cells and their derivatives as exosomes and circulating nuclear acids may become more successful in providing useful biomarkers. It is to be expected that current technical developments will contribute to the finding and validation of circulating biomarkers.
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Affiliation(s)
- Johan M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
| | - Dana M Mustafa
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
| | - Lennard J M Dekker
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
| | - Peter A E Sillevis Smitt
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
| | - Theo M Luider
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
| | - Ping-Pin Zheng
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., P.-P.Z.); Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands (L.J.M.D., P.A.E.S.S., T.M.L.); Brain Tumor Center Rotterdam, Erasmus Medical Center, Rotterdam, The Netherlands (J.M.K., D.M.M., L.J.M.D., P.A.E.S.S., T.M.L., P.-P.Z.)
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33
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Jayaram S, Gupta MK, Polisetty RV, Cho WCS, Sirdeshmukh R. Towards developing biomarkers for glioblastoma multiforme: a proteomics view. Expert Rev Proteomics 2014; 11:621-39. [PMID: 25115191 DOI: 10.1586/14789450.2014.939634] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glioblastoma multiforme (GBM) is one of the most aggressive and lethal forms of the primary brain tumors. With predominance of tumor heterogeneity and emergence of new subtypes, new approaches are needed to develop tissue-based markers for tumor typing or circulatory markers to serve as blood-based assays. Multi-omics data integration for GBM tissues would offer new insights on the molecular view of GBM pathogenesis useful to identify biomarker panels. On the other hand, mapping differentially expressed tissue proteins for their secretory potential through bioinformatics analysis or analysis of the tumor cell secretome or tumor exosomes would enhance our understanding of the tumor microenvironment and prospects for targeting circulatory biomarkers. In this review, the authors first present potential biomarker candidates for GBM that have been reported and then focus on plausible pipelines for multi-omic data integration to identify additional, high-confidence molecular panels for clinical applications in GBM.
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Affiliation(s)
- Savita Jayaram
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
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34
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Martelli C, Iavarone F, Vincenzoni F, Rossetti DV, D'Angelo L, Tamburrini G, Caldarelli M, Di Rocco C, Messana I, Castagnola M, Desiderio C. Proteomic characterization of pediatric craniopharyngioma intracystic fluid by LC-MS top-down/bottom-up integrated approaches. Electrophoresis 2014; 35:2172-83. [PMID: 24729313 DOI: 10.1002/elps.201300578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/21/2014] [Accepted: 04/04/2014] [Indexed: 02/02/2023]
Abstract
The combination of top-down and bottom-up platforms was utilized for the LC-MS proteomic characterization of the intracystic fluid of adamantinomatous craniopharyngioma pediatric brain tumor disease. Proteins and peptides characterization was achieved by high-resolution LC-ESI-LTQ-Orbitrap-MS analysis while low-resolution LC-ESI-IT-MS was applied for the complete screening of the samples and the evaluation of the protein distribution within patients. Top-down analyses were applied to liquid/liquid extracted samples while bottom-up analyses were performed after trypsin digestion of both untreated and pretreated samples. The two proteomic approaches were complementary for the characterization of the proteome of craniopharyngioma intracystic fluid. Proteins and peptides involved in inflammation, mineralization processes and lipid transport were identified, in agreement with the calcium flecks, cholesterol granules and bone residues characteristic of this fluid. Apolipoprotein A-I, A-II, C-I and J, hemoglobin fragments, ubiquitin, α-2-HS-glycoprotein or fetuin A, α-1-antichymotrypsin, vitamin D binding protein, and α-1-acid glycoprotein were characterized. These data could be relevant for the comprehension of the processes involved in the pathogenesis of the disease and the development of the cyst and could contribute to the individuation of therapeutic targets for the reduction of the cyst volume delaying and/or avoiding invasive surgical treatments.
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Affiliation(s)
- Claudia Martelli
- Facoltà di Medicina, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Rome, Italy
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35
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Shen F, Zhang Y, Yao Y, Hua W, Zhang HS, Wu JS, Zhong P, Zhou LF. Proteomic analysis of cerebrospinal fluid: toward the identification of biomarkers for gliomas. Neurosurg Rev 2014; 37:367-80; discussion 380. [PMID: 24781189 DOI: 10.1007/s10143-014-0539-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/23/2013] [Accepted: 01/19/2014] [Indexed: 11/29/2022]
Abstract
Gliomas are the most common primary brain tumors in adults and, despite advances in the understandings of glioma pathogenesis in the genetic era, they are still ineradicable, justifying the need to develop more reliable diagnostic and prognostic biomarkers for this malignancy. Because changes in cerebrospinal fluid (CSF) are suggested to be capable of sensitively reflecting pathological processes, e.g., neoplastic conditions, in the central nervous system, CSF has been deemed a valuable source for potential biomarkers screening in this era of proteomics. This systematic review focused on the proteomic analysis of glioma CSF that has been published to date and identified a total of 19 differentially expressed proteins. Further functional and protein-protein interaction assessments were performed by using Protein Analysis Through Evolutionary Relationships (PANTHER) website and Ingenuity Pathway Analysis (IPA) software, which revealed several important protein networks (e.g., IL-6/STAT-3) and four novel focus proteins (IL-6, galanin (GAL), HSPA5, and WNT4) that might be involved in glioma pathogenesis. The concentrations of these focus proteins were subsequently determined by enzyme-linked immunosorbent assay (ELISA) in an independent set of CSF and tumor cyst fluid (CF) samples. Specifically, glioblastoma (GBM) CF had significantly lower GAL, HSPA5, and WNT4 levels than CSF from different grades of glioma. In contrast, IL-6 level was significantly higher in GBM CF when compared with CSF and, among different CSF groups, was highest in GBM CSF. Therefore, these candidate protein biomarkers, identified from both the literatures and in silico analysis, may have potentials in clinical diagnosis, prognosis evaluation, treatment response monitoring, and novel therapeutic targets identification for patients with glioma.
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Affiliation(s)
- Fang Shen
- Department of Neurosurgery, Huashan Hospital, Fudan University, 12 Wurumuqi Road Middle, Shanghai, 200040, China
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36
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Samuel N, Remke M, Rutka JT, Raught B, Malkin D. Proteomic analyses of CSF aimed at biomarker development for pediatric brain tumors. J Neurooncol 2014; 118:225-238. [PMID: 24771250 DOI: 10.1007/s11060-014-1432-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/31/2014] [Indexed: 11/29/2022]
Abstract
Primary brain tumors cumulatively represent the most common solid tumors of childhood and are the leading cause of cancer related death in this age group. Traditionally, molecular findings and histological analyses from biopsies of resected tumor tissue have been used for diagnosis and classification of these diseases. However, there is a dearth of useful biomarkers that have been validated and clinically implemented for pediatric brain tumors. Notably, diseases of the central nervous system (CNS) can be assayed through analysis of cerebrospinal fluid (CSF) and as such, CSF represents an appropriate medium to obtain liquid biopsies that can be informative for diagnosis, disease classification and risk stratification. Proteomic profiling of pediatric CNS malignancies has identified putative protein markers of disease, yet few effective biomarkers have been clinically validated or implemented. Advances in protein quantification techniques have made it possible to conduct such investigations rapidly and accurately through proteome-wide analyses. This review summarizes the current literature on proteomics in pediatric neuro-oncology and discusses the implications for clinical applications of proteomics research. We also outline strategies for translating effective CSF proteomic studies into clinical applications to optimize the care of this patient population.
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Affiliation(s)
- Nardin Samuel
- MD/PhD Program, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,The Hospital for Sick Children, Toronto, ON, Canada
| | - Marc Remke
- The Hospital for Sick Children, Toronto, ON, Canada
| | - James T Rutka
- The Hospital for Sick Children, Toronto, ON, Canada.,Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,The Hospital for Sick Children, Toronto, ON, Canada. .,Department of Pediatrics, University of Toronto, Toronto, ON, Canada.
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Qualtieri A, Urso E, Pera ML, Sprovieri T, Bossio S, Gambardella A, Quattrone A. Proteomic profiling of cerebrospinal fluid in Creutzfeldt–Jakob disease. Expert Rev Proteomics 2014; 7:907-17. [DOI: 10.1586/epr.10.80] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Gollapalli K, Ray S, Srivastava R, Renu D, Singh P, Dhali S, Bajpai Dikshit J, Srikanth R, Moiyadi A, Srivastava S. Investigation of serum proteome alterations in human glioblastoma multiforme. Proteomics 2013; 12:2378-90. [PMID: 22684992 DOI: 10.1002/pmic.201200002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Glioblastoma multiforme (GBM) or grade IV astrocytoma is the most common and lethal adult malignant brain tumor. The present study was conducted to investigate the alterations in the serum proteome in GBM patients compared to healthy controls. Comparative proteomic analysis was performed employing classical 2DE and 2D-DIGE combined with MALDI TOF/TOF MS and results were further validated through Western blotting and immunoturbidimetric assay. Comparison of the serum proteome of GBM and healthy subjects revealed 55 differentially expressed and statistically significant (p <0.05) protein spots. Among the identified proteins, haptoglobin, plasminogen precursor, apolipoprotein A-1 and M, and transthyretin are very significant due to their functional consequences in glioma tumor growth and migration, and could further be studied as glioma biomarkers and grade-specific protein signatures. Analysis of the lipoprotein pattern indicated elevated serum levels of cholesterol, triacylglycerol, and low-density lipoproteins in GBM patients. Functional pathway analysis was performed using multiple software including ingenuity pathway analysis (IPA), protein analysis through evolutionary relationships (PANTHER), database for annotation, visualization and integrated discovery (DAVID), and GeneSpring to investigate the biological context of the identified proteins, which revealed the association of candidate proteins in a few essential physiological pathways such as intrinsic prothrombin activation pathway, plasminogen activating cascade, coagulation system, glioma invasiveness signaling, and PI3K signaling in B lymphocytes. A subset of the differentially expressed proteins was applied to build statistical sample class prediction models for discrimination of GBM patients and healthy controls employing partial least squares discriminant analysis (PLS-DA) and other machine learning methods such as support vector machine (SVM), Decision Tree and Naïve Bayes, and excellent discrimination between GBM and control groups was accomplished.
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Affiliation(s)
- Kishore Gollapalli
- Department of Biosciences and Bioengineering, Wadhwani Research Center for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Yamaguchi Y, Shao Z, Sharif S, Du XY, Myles T, Merchant M, Harsh G, Glantz M, Recht L, Morser J, Leung LLK. Thrombin-cleaved fragments of osteopontin are overexpressed in malignant glial tumors and provide a molecular niche with survival advantage. J Biol Chem 2012. [PMID: 23204518 DOI: 10.1074/jbc.m112.362954] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Osteopontin (OPN), which is highly expressed in malignant glioblastoma (GBM), possesses inflammatory activity modulated by proteolytic cleavage by thrombin and plasma carboxypeptidase B2 (CPB2) at a highly conserved cleavage site. Full-length OPN (OPN-FL) was elevated in cerebrospinal fluid (CSF) samples from all cancer patients compared with noncancer patients. However, thrombin-cleaved OPN (OPN-R) and thrombin/CPB2-double-cleaved OPN (OPN-L) levels were markedly increased in GBM and non-GBM gliomas compared with systemic cancer and noncancer patients. Cleaved OPN constituted ∼23 and ∼31% of the total OPN in the GBM and non-GBM CSF samples, respectively. OPN-R was also elevated in GBM tissues. Thrombin-antithrombin levels were highly correlated with cleaved OPN, but not OPN-FL, suggesting that the cleaved OPN fragments resulted from increased thrombin and CPB2 in this extracellular compartment. Levels of VEGF and CCL4 were increased in CSF of GBM and correlated with the levels of cleaved OPN. GBM cell lines were more adherent to OPN-R and OPN-L than OPN-FL. Adhesion to OPN altered gene expression, in particular genes involved with cellular processes, cell cycle regulation, death, and inflammation. OPN and its cleaved forms promoted motility of U-87 MG cells and conferred resistance to apoptosis. Although functional mutation of the RGD motif in OPN largely abolished these functions, OPN(RAA)-R regained significant cell binding and signaling function, suggesting that the SVVYGLR motif in OPN-R may substitute for the RGD motif if the latter becomes inaccessible. OPN cleavage contributes to GBM development by allowing more cells to bind in niches where they acquire anti-apoptotic properties.
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Affiliation(s)
- Yasuto Yamaguchi
- Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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Whitin JC, Jang T, Merchant M, Yu TTS, Lau K, Recht B, Cohen HJ, Recht L. Alterations in cerebrospinal fluid proteins in a presymptomatic primary glioma model. PLoS One 2012. [PMID: 23185417 PMCID: PMC3501526 DOI: 10.1371/journal.pone.0049724] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Understanding the early relationship between brain tumor cells and their environment could lead to more sensitive biomarkers and new therapeutic strategies. We have been using a rodent model of neurocarcinogenesis in which all animals develop brain tumors by six months of age to establish two early landmarks in glioma development: the appearance of a nestin+ cell at thirty days of age and the appearance of cellular hyperplasia between 60 and 120 days of age. We now report an assessment of the CSF proteome to determine the changes in protein composition that occur during this period. Materials and Methods Nestin+ cell clusters and microtumors were assessed in 63 ethylnitrosourea-exposed rats on 30, 60, and 90 days of age. CSF was obtained from the cisterna magna from 101 exposed and control rats at 30, 60, and 90 days and then analyzed using mass spectrometry. Differentially expressed peaks were isolated and identified. Results Nestin+ cells were noted in all ethylnitrosourea-exposed rats assessed pathologically. Small microtumors were noted in 0%, 18%, and 67% of 30-, 60-, and 90-day old rats, respectively (p<0.05, Chi square). False Discovery Rate analysis of peak intensities showed that the number of true discoveries with p<0.05 increased markedly with increasing age. Isolation and identification of highly differentially detected proteins at 90 days of age revealed increases in albumin and a fragment of α1 macroglobulin and alterations in glutathionylated transthyretin. Conclusions The presence of increased albumin, fragments of cerebrospinal fluid proteins, and glutathione breakdown in temporal association with the development of cellular hyperplasia, suggests that, similar to many other systemic cancers, inflammation and oxidative stress is playing an important early role in the host’s response to brain tumor development and may be involved in affecting the early growth of brain tumor.
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Affiliation(s)
- John C. Whitin
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Taichang Jang
- Department of Neurology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Milton Merchant
- Department of Neurology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tom T-S. Yu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kenneth Lau
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- The Canary Center, Department of Radiology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Benjamin Recht
- Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Harvey J. Cohen
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (LR); (HC)
| | - Lawrence Recht
- Department of Neurology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (LR); (HC)
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Fang X, Wang C, Balgley BM, Zhao K, Wang W, He F, Weil RJ, Lee CS. Targeted tissue proteomic analysis of human astrocytomas. J Proteome Res 2012; 11:3937-46. [PMID: 22794670 DOI: 10.1021/pr300303t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not only serves as a synergistic strategy to characterize low abundance proteins, but it can also be employed to conduct comparative proteomic studies of human astrocytomas. A set of fresh frozen brain biopsies were selectively microdissected to provide an enriched, high quality, and reproducible sample of tumor cells. Despite sharing many common proteins, there are significant differences in the protein expression level among different grades of astrocytomas. A large number of proteins, such as plasma membrane proteins EGFR and Erbb2, are up-regulated in glioblastoma. Besides facilitating the prioritization of follow-on biomarker selection and validation, comparative proteomics involving measurements in changes of pathways are expected to reveal the molecular relationships among different pathological grades of gliomas and potential molecular mechanisms that drive gliomagenesis.
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Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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42
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Saratsis AM, Yadavilli S, Magge S, Rood BR, Perez J, Hill DA, Hwang E, Kilburn L, Packer RJ, Nazarian J. Insights into pediatric diffuse intrinsic pontine glioma through proteomic analysis of cerebrospinal fluid. Neuro Oncol 2012; 14:547-60. [PMID: 22492959 DOI: 10.1093/neuonc/nos067] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a leading cause of brain tumor-related death in children. DIPG is not surgically resectable, resulting in a paucity of tissue available for molecular studies. As such, tumor biology is poorly understood, and, currently, there are no effective treatments. In the absence of frozen tumor specimens, body fluids--such as cerebrospinal fluid (CSF), serum, and urine--can serve as more readily accessible vehicles for detecting tumor-secreted proteins. We analyzed a total of 76 specimens, including CSF, serum, urine, and normal and tumor brainstem tissue. Protein profiling of CSF from patients with DIPG was generated by mass spectrometry using an LTQ-Orbitrap-XL and database search using the Sequest algorithm. Quantitative and statistical analyses were performed with ProteoIQ and Partek Genomics Suite. A total of 528 unique proteins were identified, 71% of which are known secreted proteins. CSF proteomic analysis revealed selective upregulation of Cyclophillin A (CypA) and dimethylarginase 1 (DDAH1) in DIPG (n = 10), compared with controls (n = 4). Protein expression was further validated with Western blot analysis and immunohistochemical assays using CSF, brain tissue, serum, and urine from DIPG and control specimens. Immunohistochemical staining showed selective upregulation of secreted but not cytosolic CypA and DDAH1 in patients with DIPG. In this study, we present the first comprehensive protein profile of CSF specimens from patients with DIPG to demonstrate selective expression of tumor proteins potentially involved in brainstem gliomagenesis. Detection of secreted CypA and DDAH1 in serum and urine has potential clinical application, with implications for assessing treatment response and detecting tumor recurrence in patients with DIPG.
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Affiliation(s)
- Amanda M Saratsis
- Department of Neurosurgery, Georgetown University Hospital, Research Center for Genetic Medicine, Children's National Medical Center NW, Washington, DC 20010, USA.
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Kalinina J, Peng J, Ritchie JC, Van Meir EG. Proteomics of gliomas: initial biomarker discovery and evolution of technology. Neuro Oncol 2011; 13:926-42. [PMID: 21852429 DOI: 10.1093/neuonc/nor078] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Gliomas are a group of aggressive brain tumors that diffusely infiltrate adjacent brain tissues, rendering them largely incurable, even with multiple treatment modalities and agents. Mostly asymptomatic at early stages, they present in several subtypes with astrocytic or oligodendrocytic features and invariably progress to malignant forms. Gliomas are difficult to classify precisely because of interobserver variability during histopathologic grading. Identifying biological signatures of each glioma subtype through protein biomarker profiling of tumor or tumor-proximal fluids is therefore of high priority. Such profiling not only may provide clues regarding tumor classification but may identify clinical biomarkers and pathologic targets for the development of personalized treatments. In the past decade, differential proteomic profiling techniques have utilized tumor, cerebrospinal fluid, and plasma from glioma patients to identify the first candidate diagnostic, prognostic, predictive, and therapeutic response markers, highlighting the potential for glioma biomarker discovery. The number of markers identified, however, has been limited, their reproducibility between studies is unclear, and none have been validated for clinical use. Recent technological advancements in methodologies for high-throughput profiling, which provide easy access, rapid screening, low sample consumption, and accurate protein identification, are anticipated to accelerate brain tumor biomarker discovery. Reliable tools for biomarker verification forecast translation of the biomarkers into clinical diagnostics in the foreseeable future. Herein we update the reader on the recent trends and directions in glioma proteomics, including key findings and established and emerging technologies for analysis, together with challenges we are still facing in identifying and verifying potential glioma biomarkers.
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Affiliation(s)
- Juliya Kalinina
- Laboratory of Molecular Neuro-Oncology, Departments of Neurosurgery, Hematology and Medical Oncology, School of Medicine, and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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Sun S, Wong TS, Zhang XQ, Pu JKS, Lee NP, Day PJR, Ng GKB, Lui WM, Leung GKK. Protein alterations associated with temozolomide resistance in subclones of human glioblastoma cell lines. J Neurooncol 2011; 107:89-100. [PMID: 21979894 PMCID: PMC3273683 DOI: 10.1007/s11060-011-0729-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 09/19/2011] [Indexed: 12/21/2022]
Abstract
Temozolomide (TMZ) is the standard chemotherapeutic agent for human malignant glioma, but intrinsic or acquired chemoresistance represents a major obstacle to successful treatment of this highly lethal group of tumours. Obtaining better understanding of the molecular mechanisms underlying TMZ resistance in malignant glioma is important for the development of better treatment strategies. We have successfully established a passage control line (D54-C10) and resistant variants (D54-P5 and D54-P10) from the parental TMZ-sensitive malignant glioma cell line D54-C0. The resistant sub-cell lines showed alterations in cell morphology, enhanced cell adhesion, increased migration capacities, and cell cycle arrests. Proteomic analysis identified a set of proteins that showed gradual changes in expression according to their 50% inhibitory concentration (IC50). Successful validation was provided by transcript profiling in another malignant glioma cell line U87-MG and its resistant counterparts. Moreover, three of the identified proteins (vimentin, cathepsin D and prolyl 4-hydroxylase, beta polypeptide) were confirmed to be upregulated in high-grade glioma. Our data suggest that acquired TMZ resistance in human malignant glioma is associated with promotion of malignant phenotypes, and our reported molecular candidates may serve not only as markers of chemoresistance but also as potential therapeutic targets in the treatment of TMZ-resistant human malignant glioma, providing a platform for future investigations.
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Affiliation(s)
- Stella Sun
- Division of Neurosurgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 21 Sassoon Road, Pokfulam, Hong Kong, People's Republic of China
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Formolo CA, Williams R, Gordish-Dressman H, MacDonald TJ, Lee NH, Hathout Y. Secretome signature of invasive glioblastoma multiforme. J Proteome Res 2011; 10:3149-59. [PMID: 21574646 DOI: 10.1021/pr200210w] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The incurability of malignant glioblastomas is mainly attributed to their highly invasive nature coupled with resistance to chemo- and radiation therapy. Because invasiveness is partially dictated by the proteins these tumors secrete we used SILAC to characterize the secretomes of four glioblastoma cell lines (LN18, T98, U118 and U87). Although U87 and U118 cells both secreted high levels of well-known invasion promoting proteins, a Matrigel invasion assay showed U87 cells to be eight times more invasive than U118 cells, suggesting that additional proteins secreted by U87 cells may contribute to the highly invasive phenotype. Indeed, we identified a number of proteins highly or exclusively expressed by U87 cells as compared to the less invasive cell lines. The most striking of these include ADAM9, ADAM10, cathepsin B, cathepsin L1, osteopontin, neuropilin-1, semaphorin-7A, suprabasin, and chitinase-3-like protein 1. U87 cells also expressed significantly low levels of some cell adhesion proteins such as periostin and EMILIN-1. Correlation of secretome profiles with relative levels of invasiveness using Pavlidis template matching further indicated potential roles for these proteins in U87 glioblastoma invasion. Antibody inhibition of CH3L1 reduced U87 cell invasiveness by 30%.
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Affiliation(s)
- Catherine A Formolo
- Research Center for Genetic Medicine, Children's National Medical Center, 111 Michigan Avenue NW, Washington, D.C. 20010, USA
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Teng PN, Bateman NW, Hood BL, Conrads TP. Advances in proximal fluid proteomics for disease biomarker discovery. J Proteome Res 2010; 9:6091-100. [PMID: 21028795 DOI: 10.1021/pr100904q] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although serum/plasma has been the preferred source for identification of disease biomarkers, these efforts have been met with little success, in large part due the relatively small number of highly abundant proteins that render the reliable detection of low abundant disease-related proteins challenging due to the expansive dynamic range of concentration of proteins in this sample. Proximal fluid, the fluid derived from the extracellular milieu of tissues, contains a large repertoire of shed and secreted proteins that are likely to be present at higher concentrations relative to plasma/serum. It is hypothesized that many, if not all, proximal fluid proteins exchange with peripheral circulation, which has provided significant motivation for utilizing proximal fluids as a primary sample source for protein biomarker discovery. The present review highlights recent advances in proximal fluid proteomics, including the various protocols utilized to harvest proximal fluids along with detailing the results from mass spectrometry- and antibody-based analyses.
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Affiliation(s)
- Pang-ning Teng
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
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47
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Hays JL, Kim G, Giuroiu I, Kohn EC. Proteomics and ovarian cancer: integrating proteomics information into clinical care. J Proteomics 2010; 73:1864-72. [PMID: 20561909 DOI: 10.1016/j.jprot.2010.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 05/20/2010] [Accepted: 05/25/2010] [Indexed: 01/03/2023]
Abstract
The power of proteomics allows unparalleled opportunity to query the molecular mechanisms of a malignant cell and the tumor microenvironment in patients with ovarian cancer and other solid tumors. This information has given us insight into the perturbations of signaling pathways within tumor cells and has aided the discovery of new drug targets for the tumor and possible prognostic indicators of outcome and disease response to therapy. Proteomics analysis of serum and ascites has also given us sources with which to discover possible early markers for the presence of new disease and for the progression of established cancer throughout the course of treatment. Unfortunately, this wealth of information has yielded little to date in changing the clinical care of these patients from a diagnostic, prognostic, or treatment perspective. The rational examination and translation of proteomics data in the context of past clinical trials and the design of future clinical trials must occur before we can march forward into the future of personalized medicine.
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Affiliation(s)
- John L Hays
- Molecular Signaling Section, Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1906, USA.
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Niclou SP, Fack F, Rajcevic U. Glioma proteomics: status and perspectives. J Proteomics 2010; 73:1823-38. [PMID: 20332038 DOI: 10.1016/j.jprot.2010.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Revised: 03/11/2010] [Accepted: 03/17/2010] [Indexed: 12/17/2022]
Abstract
High grade gliomas are the most common brain tumors in adults and their malignant nature makes them the fourth biggest cause of cancer death. Major efforts in neuro-oncology research are needed to reach similar progress in treatment efficacy as that achieved for other cancers in recent years. In addition to the urgent need to identify novel effective drug targets against malignant gliomas, the search for glioma biomarkers and grade specific protein signatures will provide a much needed contribution to diagnosis, prognosis, treatment decision and assessment of treatment response. Over the past years glioma proteomics has been attempted at different levels, including proteome analysis of patient biopsies and bodily fluids, of glioma cell lines and animal models. Here we provide an extensive review of the outcome of these studies in terms of protein identifications (protein numbers and regulated proteins), with an emphasis on the methods used and the limitations of the studies with regard to biomarker discovery. This is followed by a perspective on novel technologies and on the potential future contribution of proteomics in a broad sense to understanding glioma biology.
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Affiliation(s)
- Simone P Niclou
- Norlux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg, Luxembourg.
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